# ClinicalMatch AI — Agent Instructions

> Project memory (build state, completed features, constraints) is also tracked in `.claude/project_memory.md` in this repo.

This is a hackathon submission for **"Agents Assemble: Healthcare AI Endgame Challenge"** on the Prompt Opinion platform. Judging criteria: MCP compliance, A2A workflow, FHIR R4 standards, AI quality, impact, feasibility.

## Stack at a glance

| Layer | Technology |
|---|---|
| Backend | FastAPI (Python 3.12), uvicorn |
| Graph DB | Neo4j Community 5.x via bolt |
| LLM | claude-opus-4-7 via aimlapi.com (OpenAI-compatible) |
| GraphRAG | LangChain `GraphCypherQAChain` + custom Cypher prompt |
| Frontend | Next.js 16 (webpack mode), React 19, Tailwind CSS 3, Recharts, Leaflet |
| Standards | FHIR R4 · MCP (stdio) · A2A state machine |

## Critical: LLM API

**Never use the Anthropic SDK directly.** All LLM calls go through aimlapi.com or a compatible alternative using the OpenAI-compatible interface:

```python
from openai import OpenAI

client = OpenAI(
    api_key=os.getenv("OPENAI_API_KEY"),
    base_url=os.getenv("OPENAI_BASE_URL", "https://ai.aimlapi.com/v1"),
)
model = os.getenv("OPENAI_MODEL", "claude-opus-4-7")
```

See `backend/llm_client.py` for the canonical pattern. Do not add `import anthropic` anywhere.

## Starting the services

```bash
# Backend — always use --reload for hot reload
cd backend && source venv/bin/activate
uvicorn main:app --reload --port 8000

# Frontend — always use --webpack (Turbopack is broken on this system)
cd frontend && npm run dev   # runs: next dev --webpack

# MCP server (separate process, stdio transport)
cd backend && python mcp_server.py

# Seed graph data (~15 min first run)
curl -X POST http://localhost:8000/seed
```

After changing backend Python files, uvicorn `--reload` should pick them up. If a 404 appears for a newly-added endpoint or old errors persist, the server needs a manual restart — kill the process and re-run the uvicorn command.

## Project layout

```
promptop/
├── CLAUDE.md                   ← you are here
├── README.md                   ← user-facing docs
├── backend/
│   ├── main.py                 ← FastAPI app, all routes
│   ├── clinicaltrials_api.py   ← ClinicalTrials.gov v2 API (async + sync)
│   ├── intake_matching.py      ← SI-unit clinical intake → trial scoring
│   ├── trial_enrichment.py     ← passive graph enrichment on search
│   ├── matching_engine.py      ← FHIR patient → trial scoring (LLM-assisted)
│   ├── a2a_workflow.py         ← A2A state machine (INGEST→PARSE→MATCH→SCORE→RECRUIT)
│   ├── graphrag.py             ← LangChain GraphCypherQAChain with custom prompt
│   ├── graph_seeder.py         ← seeds 500 patients + real NCT trials from APIs
│   ├── fhir_adapter.py         ← FHIR R4 patient models (P001–P005 mock patients)
│   ├── neo4j_setup.py          ← Neo4j connection + schema setup
│   ├── analytics.py            ← dashboard KPIs, funnel, demographics, map data
│   ├── recruitment_pipeline.py ← kanban board, outreach generation
│   ├── llm_client.py           ← all LLM calls (aimlapi.com / claude-opus-4-7)
│   ├── mcp_server.py           ← MCP stdio server (6 tools)
│   └── requirements.txt
├── frontend/
│   ├── src/app/
│   │   ├── page.tsx            ← Trial Finder (real-time CT.gov, recency sort)
│   │   ├── intake/page.tsx     ← Eligibility Check (SI-unit clinical intake form)
│   │   ├── screening/page.tsx  ← Patient Screening (A2A pipeline, FHIR patients)
│   │   ├── recruitment/page.tsx← Recruitment Hub (kanban + outreach generation)
│   │   ├── dashboard/page.tsx  ← Analytics dashboard (Recharts)
│   │   ├── map/page.tsx        ← Leaflet site map
│   │   ├── graph/page.tsx      ← GraphRAG natural language query
│   │   └── layout.tsx          ← App shell with Sidebar
│   ├── src/components/
│   │   ├── Sidebar.tsx         ← Navigation sidebar
│   │   └── MapComponent.tsx    ← Raw Leaflet map (no react-leaflet SSR issues)
│   ├── src/lib/api.ts          ← Typed API client for all backend endpoints
│   └── next.config.ts          ← webpack mode, filesystem cache, optimizePackageImports
└── docker/                     ← Docker + Nginx for HuggingFace Spaces deployment
```

## Neo4j graph schema

```
(Patient)         id, name, age, sex, ecog, condition, city, state, ethnicity,
                  biomarkers[], medications[], source, stage
(Trial)           id (NCT), title, condition, phase, status, sponsor,
                  eligibility_criteria, min_age, max_age, sex, enrollment,
                  start_date, completion_date, last_updated, ctgov_url
(Diagnosis)       id, name, icd10
(Biomarker)       id (e.g. HER2_POS), name (e.g. "HER2 Positive")
(Medication)      id (e.g. TAMOXIFEN), name
(StudySite)       id, name, city, state, lat, lon, trials, enrolled, capacity

Relationships:
  (Patient)-[:ELIGIBLE_FOR {score}]->(Trial)
  (Patient)-[:HAS_DIAGNOSIS]->(Diagnosis)
  (Patient)-[:HAS_BIOMARKER]->(Biomarker)
  (Patient)-[:TAKES_MEDICATION]->(Medication)
  (Trial)-[:LOCATED_AT]->(StudySite)
```

**Graph scale after seeding:** ~500 patients, ~250 trials, ~9,100 ELIGIBLE_FOR edges.

Patient IDs from seeder: `P_C50_0001` (breast), `P_C61_0001` (prostate), etc.
Mock FHIR patients: `P001`–`P005` (used by screening/workflow pages).

## Key backend modules

### `clinicaltrials_api.py`
- `search_trials()` — async, `sort=LastUpdatePostDate:desc`
- `get_trial_details()` — async
- `search_trials_sync()` / `get_trial_details_sync()` — sync using `httpx.Client` (NOT `asyncio.run()`). Safe to call from both sync functions and FastAPI async handlers.
- `_normalize_study()` — extracts `last_updated`, `ctgov_url` in addition to core fields.

**Do not** use `asyncio.run()` inside these sync wrappers — it breaks when called from a running FastAPI event loop. The sync wrappers use `httpx.Client` directly.

### `intake_matching.py`
Implements SI-unit clinical intake → trial eligibility matching without requiring a patient ID:
- `BIOMARKER_REGISTRY` — maps graph node IDs to labels and eligibility text search terms
- `score_intake_against_trial()` — weighted scoring: age (25), sex (15), ECOG (15), biomarkers (30), labs (15)
- `_check_labs()` — parses thresholds from eligibility criteria text, converts SI units (creatinine μmol/L ↔ mg/dL, bilirubin μmol/L ↔ mg/dL)
- `save_intake_as_patient()` — persists intake as `Patient` node for long-term graph enrichment

### `trial_enrichment.py`
- `enrich_trials_from_search()` — called as a `BackgroundTask` on every `/api/v1/trials/search` response; upserts Trial + StudySite nodes
- `get_eligible_patient_counts()` — batch graph query, returns `{nct_id: count}`
- `get_graph_intelligence()` — per-trial: eligible count + top biomarkers + similar trials

### `graphrag.py`
Uses a custom `_CYPHER_PROMPT` with explicit schema examples. Critical rules in the prompt:
- Biomarker lookups use `id` property (`{id: 'HER2_POS'}`), never `{name: 'HER2', status: 'positive'}`
- Condition lookups use lowercase on Trial nodes
- Patient eligibility always via `(Patient)-[:ELIGIBLE_FOR]->(Trial)`

### `a2a_workflow.py`
Five-state machine: `INGESTING → PARSING_PROTOCOL → MATCHING → SCORING → RECRUITING`
- Calls `search_trials_sync()` / `get_trial_details_sync()` — these are safe (use httpx.Client)
- `run_pipeline()` is synchronous; called from async FastAPI endpoint without `await`

## Key frontend pages

### `/intake` — Eligibility Check
The primary self-service interface. Accepts raw clinical data in SI units; no patient ID needed.
- Six sections: Diagnosis & Demographics, Biomarkers, Lab Values, Treatment History
- Biomarker registry loaded from `GET /api/v1/intake/biomarkers`
- Submits to `POST /api/v1/intake/match`
- Optional "Save to graph" checkbox persists profile as Patient node

### `/` — Trial Finder
- Sorted by `LastUpdatePostDate:desc` (most recently updated first)
- Each search result triggers background graph enrichment
- Expanded cards show Graph Intelligence panel: eligible patient count, top biomarkers, similar trials
- Direct ClinicalTrials.gov link per trial

### `/screening` — Patient Screening
- Patient ID field is a `<input list="...">` combobox loading from `GET /api/v1/graph/patients`
- NCT ID field is a combobox with quick-pick suggestions
- Validates non-empty inputs before submitting
- Two modes: Single Trial Screen and A2A Full Pipeline

## API endpoints (key ones)

```
GET  /api/v1/trials/search          — real-time CT.gov search, sorted by recency, graph-enriched
POST /api/v1/intake/match           — SI-unit clinical intake → ranked trial matches
GET  /api/v1/intake/biomarkers      — biomarker registry for the intake form
GET  /api/v1/trials/{nct_id}/intelligence — graph-derived insights per trial
GET  /api/v1/graph/patients         — query Neo4j for seeded patient IDs
POST /api/v1/patients/{id}/screen/{nct_id} — screen FHIR patient against trial
POST /api/v1/workflow/run           — run full A2A pipeline
GET  /api/v1/analytics/kpi         — dashboard KPIs
GET  /api/v1/map/data               — site coordinates + patient clusters
POST /api/v1/graph/query            — GraphRAG natural language
POST /seed                          — trigger full graph seeding
GET  /api/v1/graph/stats            — node/edge counts
```

Full interactive docs at `http://localhost:8000/docs`.

## Environment variables

```env
NEO4J_URI=bolt://localhost:7687
NEO4J_USERNAME=neo4j
NEO4J_PASSWORD=clinicalmatch2024
NEO4J_DATABASE=neo4j

OPENAI_API_KEY=<aimlapi.com key>
OPENAI_BASE_URL=https://ai.aimlapi.com/v1
OPENAI_MODEL=claude-opus-4-7

NEXT_PUBLIC_API_URL=http://localhost:8000   # dev only; empty string in Docker
```

## Known issues and constraints

- **Turbopack is broken** on this machine — always use `next dev --webpack`. Never suggest `next dev` without `--webpack`.
- **`next/font/google`** causes compilation to hang (network request during bundling). Geist font is installed as a package but the `next/font/google` import is removed. Use plain Tailwind `font-sans`.
- **`asyncio.run()` from async context** — the sync CT.gov wrappers use `httpx.Client` to avoid this. Never re-introduce `asyncio.run()` into the sync wrappers; it will fail when called from FastAPI's running event loop.
- **Leaflet SSR** — `MapComponent.tsx` uses raw Leaflet (not react-leaflet) via `useEffect`. The `MapComponent` dynamic import has `ssr: false`. Do not switch to react-leaflet's `MapContainer`.
- **`suppressHydrationWarning`** on `<body>` in `layout.tsx` — required for Grammarly browser extension compatibility.
- **Mock FHIR patients** (P001–P005) live in `fhir_adapter.py`. The 500 seeded graph patients (`P_C50_0001` etc.) are in Neo4j only. The screening page loads graph patients from `GET /api/v1/graph/patients` for the combobox.

## Adding new features

1. **New backend route**: add to `main.py`, import the module at the top, add a Pydantic request model if needed
2. **New API function**: add a typed function to `frontend/src/lib/api.ts`
3. **New page**: create `frontend/src/app/<name>/page.tsx`, add to `nav` array in `Sidebar.tsx`
4. **Graph schema change**: update `neo4j_setup.py` constraints/indexes, update `_CYPHER_PROMPT` in `graphrag.py` with the new node/property examples
5. **New biomarker**: add to `BIOMARKER_REGISTRY` in `intake_matching.py` and to `BM_GROUPS` in `frontend/src/app/intake/page.tsx`

## Demo script (for judges)

1. `GET /api/v1/graph/stats` — confirm 500+ patients and 9,100+ edges
2. `/` — search "breast cancer" → observe recency sort, graph-matched patient count badges
3. Expand a trial → Graph Intelligence panel shows eligible patients, top biomarkers, similar trials
4. `/intake` — enter: Age 52, Female, ECOG 1, HER2+, Hgb 12.5 g/dL, Creatinine 88 μmol/L → ranked trials with pass/fail breakdown
5. `/screening` — select P_C50_0001 from combobox → run A2A Pipeline → observe 5-state machine
6. `/recruitment` — kanban board, generate PCP letter outreach
7. `/dashboard` — KPI cards, enrollment funnel, demographics
8. `/graph` — ask "which patients are eligible for breast cancer trials?"
9. In Prompt Opinion: call MCP tool `find_trials(condition="breast cancer")`